Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species representing 98% of tribes, a 35-fold increase in gene sampling and 3-fold increase in taxon sampling over previous studies [4]. Most data were generated with a new anchored hybrid enrichment (AHE) [5] gene kit (BUTTERFLY1.0) that includes both new and frequently used (e.g., [6]) informative loci, enabling direct comparison and future dataset merging with previous studies. Butterflies originated around 119 million years ago (mya) in the late Cretaceous, but most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass-extinction 65 mya. Our analyses support swallowtails (Papilionidae) as sister to all other butterflies, followed by skippers (Hesperiidae) + the nocturnal butterflies (Hedylidae) as sister to the remainder, indicating a secondary reversal from diurnality to nocturnality. The whites (Pieridae) were strongly supported as sister to brush-footed butterflies (Nymphalidae) and blues + metalmarks (Lycaenidae and Riodinidae). Ant association independently evolved once in Lycaenidae and twice in Riodinidae. This study overturns prior notions of the taxon's evolutionary history, as many long-recognized subfamilies and tribes are para- or polyphyletic. It also provides a much-needed backbone for a revised classification of butterflies and for future comparative studies including genome evolution and ecology.

The age, geographic origin and time of major radiation of the butterflies (Hesperioidea + Papilionoidea + Hedyloidea) are largely unknown. The general modern view is that butterflies arose during the Late Jurassic/Cretaceous in the southern hemisphere (southern Pangea/Gondwana before continental breakup), but this is not universally accepted, and is a best guess based largely on circumstantial evidence. The extreme paucity of fossils and lack of modern, higher-level phylogenies of extant monophyletic groups have been major impediments towards determining reliable estimates of either their age or geographic origin. Here we present a phylogenetic and historical biogeographic analysis of a higher butterfly taxon, the swallowtail tribe Troidini. We analysed molecular data for three protein-encoding genes, mitochondrial ND5 and COI–COII, and nuclear EF–1α, both separately and in combination using maximum parsimony (with and without character weighting and transition/transversion weighting), maximum likelihood and Bayesian methods. Our sample included representatives of all 10 genera of Troidini and distant ingroup taxa (Baroniinae, Parnassiinae, Graphiini, Papilionini), with Pieridae as outgroup. Analysis of the combined dataset (4326 bp; 1012 parsimony informative characters) recovered the Troidini as a well supported monophyletic group and the monophyly of its two subtribes, Battina and Troidina. The most parsimonious biogeographic hypothesis suggests a southern origin of the tribe in remnant Gondwana (Madagascar–Greater India–Australia–Antarctica–South America) sometime after the rifting and final separation of Africa in the Late Cretaceous (<90 Mya). Although an ancient vicariance pattern is proposed, at least four relatively recent dispersal/extinction events are needed to reconcile anomalies in distribution, most of which can be explained by geological and climatic events in South-east Asia and Australia during the late Tertiary. Application of a molecular clock based on a rate smoothing programme to estimate various divergence times based on vicariance events, revealed two peculiarities in our biogeographic vicariance model that do not strictly accord with current understanding of the temporal breakup of Gondwana: (1) the troidine fauna of Greater India did not become isolated from Gondwana (Antarctica) until the end of the Cretaceous (c. 65 Mya), well after Madagascar separated from Greater India (84 Mya); and (2) the faunas of Greater India, Australia and South America diverged simultaneously, also at the K/T boundary. A recent published estimate of the time (31 Mya) of divergence between Cressida Swainson (Australia) and Euryades Felder & Felder (South America) is shown to be in error.

A comprehensive and critical review of all available literature on associations between Australian lycaenid butterflies and ants was undertaken to establish an accurate database of the partners involved. Collections and observations of lycaenids and ants were used to augment this review, resulting in a significant number of newly documented association (and non-association) records. Twenty published records considered to be erroneous or doubtful are noted, with justifications given for their deletion from the association database. In total, 265 different associations between lycaenids and ants, plus 65 non-attendance records are documented for Australia. Nearly 80% of the lycaenid species in Australia, for which the early stages are known, are recorded associating with ants and half of these are obligately ant-associated. Patterns of association are examined from the perspective of both lycaenids and ants, with a focus on ant systematics and ecology. Lycaenids are recorded with five ant subfamilies, including the first record of an association with the Pseudomyrmecinae. The Dolichoderinae, and to some extent the Formicinae, have a disproportionately high percentage of genera that associate with lycaenid butterflies. All ant species that tend lycaenids spend at least some portion of their time foraging on vegetation to collect plant and insect nectar. There is a robust relationship between the competitive status of ants within a community, and their frequency and degree of association with lycaenids. Obligate ant-association is accompanied by a high degree of specificity for ant partner, but two notable exceptions, Ogyris aenone and O. amaryllis are discussed. Facultative myrmecophiles tend to associate with a broad range of ants, although interactions with ecologically dominant ants are less frequent than might be expected based on the abundance of dominant ant species in Australian communities.

Butterflies are a diverse and charismatic insect group that are thought to have evolved with plants and dispersed throughout the world in response to key geological events. However, these hypotheses have not been extensively tested because a comprehensive phylogenetic framework and datasets for butterfly larval hosts and global distributions are lacking. We sequenced 391 genes from nearly 2,300 butterfly species, sampled from 90 countries and 28 specimen collections, to reconstruct a new phylogenomic tree of butterflies representing 92% of all genera. Our phylogeny has strong support for nearly all nodes and demonstrates that at least 36 butterfly tribes require reclassification. Divergence time analyses imply an origin ~100 million years ago for butterflies and indicate that all but one family were present before the K/Pg extinction event. We aggregated larval host datasets and global distribution records and found that butterflies are likely to have first fed on Fabaceae and originated in what is now the Americas. Soon after the Cretaceous Thermal Maximum, butterflies crossed Beringia and diversified in the Palaeotropics. Our results also reveal that most butterfly species are specialists that feed on only one larval host plant family. However, generalist butterflies that consume two or more plant families usually feed on closely related plants.